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[codex] Improve agent runtime recovery and governance (#4086)
## Thinking Path > - Paperclip orchestrates AI agents for zero-human companies. > - The heartbeat runtime, agent import path, and agent configuration defaults determine whether work is dispatched safely and predictably. > - Several accumulated fixes all touched agent execution recovery, wake routing, import behavior, and runtime concurrency defaults. > - Those changes need to land together so the heartbeat service and agent creation defaults stay internally consistent. > - This pull request groups the runtime/governance changes from the split branch into one standalone branch. > - The benefit is safer recovery for stranded runs, bounded high-volume reads, imported-agent approval correctness, skill-template support, and a clearer default concurrency policy. ## What Changed - Fixed stranded continuation recovery so successful automatic retries are requeued instead of incorrectly blocking the issue. - Bounded high-volume issue/log reads across issue, heartbeat, agent, project, and workspace paths. - Fixed imported-agent approval and instruction-path permission handling. - Quarantined seeded worktree execution state during worktree provisioning. - Queued approval follow-up wakes and hardened SQL_ASCII heartbeat output handling. - Added reusable agent instruction templates for hiring flows. - Set the default max concurrent agent runs to five and updated related UI/tests/docs. ## Verification - `pnpm install --frozen-lockfile` - `pnpm exec vitest run server/src/__tests__/company-portability.test.ts server/src/__tests__/heartbeat-process-recovery.test.ts server/src/__tests__/heartbeat-comment-wake-batching.test.ts server/src/__tests__/heartbeat-list.test.ts server/src/__tests__/issues-service.test.ts server/src/__tests__/agent-permissions-routes.test.ts packages/adapter-utils/src/server-utils.test.ts ui/src/lib/new-agent-runtime-config.test.ts` - Split integration check: merged this branch first, followed by the other [PAP-1614](/PAP/issues/PAP-1614) branches, with no merge conflicts. - Confirmed this branch does not include `pnpm-lock.yaml`. ## Risks - Medium risk: touches heartbeat recovery, queueing, and issue list bounds in central runtime paths. - Imported-agent and concurrency default behavior changes may affect existing automation that assumes one-at-a-time default runs. - No database migrations are included. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - OpenAI Codex, GPT-5.4 tool-enabled coding model, agentic code-editing/runtime with local shell and GitHub CLI access; exact context window and reasoning mode are not exposed by the Paperclip harness. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] If this change affects the UI, I have included before/after screenshots - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>
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38 changed files with 1569 additions and 240 deletions
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@ -38,6 +38,9 @@ import { getDefaultCompanyGoal } from "./goals.js";
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const ALL_ISSUE_STATUSES = ["backlog", "todo", "in_progress", "in_review", "blocked", "done", "cancelled"];
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const MAX_ISSUE_COMMENT_PAGE_LIMIT = 500;
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export const ISSUE_LIST_DEFAULT_LIMIT = 500;
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export const ISSUE_LIST_MAX_LIMIT = 1000;
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const ISSUE_LIST_RELATED_QUERY_CHUNK_SIZE = 500;
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export const MAX_CHILD_ISSUES_CREATED_BY_HELPER = 25;
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const MAX_CHILD_COMPLETION_SUMMARIES = 20;
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const CHILD_COMPLETION_SUMMARY_BODY_MAX_CHARS = 500;
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@ -106,6 +109,10 @@ type IssueUserCommentStats = {
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myLastCommentAt: Date | null;
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lastExternalCommentAt: Date | null;
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};
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type IssueReadStat = {
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issueId: string;
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myLastReadAt: Date | null;
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};
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type IssueLastActivityStat = {
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issueId: string;
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latestCommentAt: Date | null;
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@ -158,6 +165,18 @@ function escapeLikePattern(value: string): string {
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return value.replace(/[\\%_]/g, "\\$&");
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}
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export function clampIssueListLimit(limit: number): number {
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return Math.min(ISSUE_LIST_MAX_LIMIT, Math.max(1, Math.floor(limit)));
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}
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function chunkList<T>(values: T[], size: number): T[][] {
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const chunks: T[][] = [];
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for (let index = 0; index < values.length; index += size) {
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chunks.push(values.slice(index, index + size));
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}
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return chunks;
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}
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function truncateInlineSummary(value: string | null | undefined, maxChars = CHILD_COMPLETION_SUMMARY_BODY_MAX_CHARS) {
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const normalized = value?.trim();
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if (!normalized) return null;
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@ -494,20 +513,22 @@ function latestIssueActivityAt(...values: Array<Date | string | null | undefined
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async function labelMapForIssues(dbOrTx: any, issueIds: string[]): Promise<Map<string, IssueLabelRow[]>> {
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const map = new Map<string, IssueLabelRow[]>();
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if (issueIds.length === 0) return map;
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const rows = await dbOrTx
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.select({
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issueId: issueLabels.issueId,
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label: labels,
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})
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.from(issueLabels)
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.innerJoin(labels, eq(issueLabels.labelId, labels.id))
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.where(inArray(issueLabels.issueId, issueIds))
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.orderBy(asc(labels.name), asc(labels.id));
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for (const issueIdChunk of chunkList(issueIds, ISSUE_LIST_RELATED_QUERY_CHUNK_SIZE)) {
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const rows = await dbOrTx
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.select({
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issueId: issueLabels.issueId,
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label: labels,
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})
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.from(issueLabels)
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.innerJoin(labels, eq(issueLabels.labelId, labels.id))
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.where(inArray(issueLabels.issueId, issueIdChunk))
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.orderBy(asc(labels.name), asc(labels.id));
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for (const row of rows) {
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const existing = map.get(row.issueId);
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if (existing) existing.push(row.label);
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else map.set(row.issueId, [row.label]);
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for (const row of rows) {
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const existing = map.get(row.issueId);
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if (existing) existing.push(row.label);
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else map.set(row.issueId, [row.label]);
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}
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}
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return map;
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}
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@ -537,27 +558,29 @@ async function activeRunMapForIssues(
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.filter((id): id is string => id != null);
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if (runIds.length === 0) return map;
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const rows = await dbOrTx
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.select({
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id: heartbeatRuns.id,
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status: heartbeatRuns.status,
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agentId: heartbeatRuns.agentId,
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invocationSource: heartbeatRuns.invocationSource,
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triggerDetail: heartbeatRuns.triggerDetail,
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startedAt: heartbeatRuns.startedAt,
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finishedAt: heartbeatRuns.finishedAt,
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createdAt: heartbeatRuns.createdAt,
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})
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.from(heartbeatRuns)
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.where(
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and(
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inArray(heartbeatRuns.id, runIds),
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inArray(heartbeatRuns.status, ACTIVE_RUN_STATUSES),
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),
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);
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for (const runIdChunk of chunkList([...new Set(runIds)], ISSUE_LIST_RELATED_QUERY_CHUNK_SIZE)) {
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const rows = await dbOrTx
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.select({
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id: heartbeatRuns.id,
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status: heartbeatRuns.status,
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agentId: heartbeatRuns.agentId,
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invocationSource: heartbeatRuns.invocationSource,
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triggerDetail: heartbeatRuns.triggerDetail,
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startedAt: heartbeatRuns.startedAt,
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finishedAt: heartbeatRuns.finishedAt,
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createdAt: heartbeatRuns.createdAt,
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})
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.from(heartbeatRuns)
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.where(
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and(
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inArray(heartbeatRuns.id, runIdChunk),
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inArray(heartbeatRuns.status, ACTIVE_RUN_STATUSES),
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),
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);
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for (const row of rows) {
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map.set(row.id, row);
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for (const row of rows) {
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map.set(row.id, row);
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}
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}
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return map;
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}
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@ -617,6 +640,131 @@ function withActiveRuns(
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}));
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}
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async function userCommentStatsForIssues(
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dbOrTx: any,
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companyId: string,
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userId: string,
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issueIds: string[],
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): Promise<IssueUserCommentStats[]> {
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const stats: IssueUserCommentStats[] = [];
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for (const issueIdChunk of chunkList(issueIds, ISSUE_LIST_RELATED_QUERY_CHUNK_SIZE)) {
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const rows = await dbOrTx
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.select({
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issueId: issueComments.issueId,
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myLastCommentAt: sql<Date | null>`
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MAX(CASE WHEN ${issueComments.authorUserId} = ${userId} THEN ${issueComments.createdAt} END)
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`,
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lastExternalCommentAt: sql<Date | null>`
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MAX(
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CASE
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WHEN ${issueComments.authorUserId} IS NULL OR ${issueComments.authorUserId} <> ${userId}
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THEN ${issueComments.createdAt}
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END
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)
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`,
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})
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.from(issueComments)
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.where(
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and(
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eq(issueComments.companyId, companyId),
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inArray(issueComments.issueId, issueIdChunk),
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),
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)
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.groupBy(issueComments.issueId);
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stats.push(...rows);
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}
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return stats;
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}
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async function userReadStatsForIssues(
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dbOrTx: any,
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companyId: string,
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userId: string,
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issueIds: string[],
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): Promise<IssueReadStat[]> {
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const stats: IssueReadStat[] = [];
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for (const issueIdChunk of chunkList(issueIds, ISSUE_LIST_RELATED_QUERY_CHUNK_SIZE)) {
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const rows = await dbOrTx
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.select({
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issueId: issueReadStates.issueId,
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myLastReadAt: issueReadStates.lastReadAt,
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})
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.from(issueReadStates)
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.where(
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and(
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eq(issueReadStates.companyId, companyId),
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eq(issueReadStates.userId, userId),
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inArray(issueReadStates.issueId, issueIdChunk),
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),
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);
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stats.push(...rows);
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}
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return stats;
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}
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async function lastActivityStatsForIssues(
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dbOrTx: any,
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companyId: string,
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issueIds: string[],
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): Promise<IssueLastActivityStat[]> {
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const byIssueId = new Map<string, IssueLastActivityStat>();
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for (const issueIdChunk of chunkList(issueIds, ISSUE_LIST_RELATED_QUERY_CHUNK_SIZE)) {
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const [commentRows, logRows] = await Promise.all([
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dbOrTx
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.select({
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issueId: issueComments.issueId,
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latestCommentAt: sql<Date | null>`MAX(${issueComments.createdAt})`,
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})
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.from(issueComments)
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.where(
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and(
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eq(issueComments.companyId, companyId),
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inArray(issueComments.issueId, issueIdChunk),
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),
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)
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.groupBy(issueComments.issueId),
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dbOrTx
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.select({
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issueId: activityLog.entityId,
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latestLogAt: sql<Date | null>`MAX(${activityLog.createdAt})`,
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})
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.from(activityLog)
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.where(
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and(
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eq(activityLog.companyId, companyId),
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eq(activityLog.entityType, "issue"),
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inArray(activityLog.entityId, issueIdChunk),
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sql`${activityLog.action} NOT IN (${sql.join(
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ISSUE_LOCAL_INBOX_ACTIVITY_ACTIONS.map((action) => sql`${action}`),
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sql`, `,
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)})`,
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),
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)
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.groupBy(activityLog.entityId),
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]);
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for (const row of commentRows) {
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byIssueId.set(row.issueId, {
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issueId: row.issueId,
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latestCommentAt: row.latestCommentAt,
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latestLogAt: null,
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});
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}
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for (const row of logRows) {
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const existing = byIssueId.get(row.issueId);
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if (existing) existing.latestLogAt = row.latestLogAt;
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else {
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byIssueId.set(row.issueId, {
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issueId: row.issueId,
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latestCommentAt: null,
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latestLogAt: row.latestLogAt,
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});
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}
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}
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}
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return [...byIssueId.values()];
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}
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export function issueService(db: Db) {
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const instanceSettings = instanceSettingsService(db);
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@ -1105,99 +1253,12 @@ export function issueService(db: Db) {
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const issueIds = withRuns.map((row) => row.id);
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const [statsRows, readRows, lastActivityRows] = await Promise.all([
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contextUserId
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? db
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.select({
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issueId: issueComments.issueId,
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myLastCommentAt: sql<Date | null>`
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MAX(CASE WHEN ${issueComments.authorUserId} = ${contextUserId} THEN ${issueComments.createdAt} END)
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`,
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lastExternalCommentAt: sql<Date | null>`
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MAX(
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CASE
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WHEN ${issueComments.authorUserId} IS NULL OR ${issueComments.authorUserId} <> ${contextUserId}
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THEN ${issueComments.createdAt}
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END
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)
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`,
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})
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.from(issueComments)
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.where(
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and(
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eq(issueComments.companyId, companyId),
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inArray(issueComments.issueId, issueIds),
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),
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)
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.groupBy(issueComments.issueId)
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? userCommentStatsForIssues(db, companyId, contextUserId, issueIds)
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: Promise.resolve([]),
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contextUserId
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? db
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.select({
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issueId: issueReadStates.issueId,
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myLastReadAt: issueReadStates.lastReadAt,
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})
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.from(issueReadStates)
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.where(
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and(
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eq(issueReadStates.companyId, companyId),
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eq(issueReadStates.userId, contextUserId),
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inArray(issueReadStates.issueId, issueIds),
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),
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)
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? userReadStatsForIssues(db, companyId, contextUserId, issueIds)
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: Promise.resolve([]),
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Promise.all([
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db
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.select({
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issueId: issueComments.issueId,
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latestCommentAt: sql<Date | null>`MAX(${issueComments.createdAt})`,
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})
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.from(issueComments)
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.where(
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and(
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eq(issueComments.companyId, companyId),
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inArray(issueComments.issueId, issueIds),
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),
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)
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.groupBy(issueComments.issueId),
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db
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.select({
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issueId: activityLog.entityId,
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latestLogAt: sql<Date | null>`MAX(${activityLog.createdAt})`,
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})
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.from(activityLog)
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.where(
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and(
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eq(activityLog.companyId, companyId),
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eq(activityLog.entityType, "issue"),
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inArray(activityLog.entityId, issueIds),
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sql`${activityLog.action} NOT IN (${sql.join(
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ISSUE_LOCAL_INBOX_ACTIVITY_ACTIONS.map((action) => sql`${action}`),
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sql`, `,
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)})`,
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),
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)
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.groupBy(activityLog.entityId),
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]).then(([commentRows, logRows]) => {
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const byIssueId = new Map<string, IssueLastActivityStat>();
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for (const row of commentRows) {
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byIssueId.set(row.issueId, {
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issueId: row.issueId,
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latestCommentAt: row.latestCommentAt,
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latestLogAt: null,
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});
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}
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for (const row of logRows) {
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const existing = byIssueId.get(row.issueId);
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if (existing) existing.latestLogAt = row.latestLogAt;
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else {
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byIssueId.set(row.issueId, {
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issueId: row.issueId,
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latestCommentAt: null,
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latestLogAt: row.latestLogAt,
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});
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}
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}
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return [...byIssueId.values()];
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}),
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lastActivityStatsForIssues(db, companyId, issueIds),
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]);
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const statsByIssueId = new Map(statsRows.map((row) => [row.issueId, row]));
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const lastActivityByIssueId = new Map(lastActivityRows.map((row) => [row.issueId, row]));
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